The generation of cell diversity in the central nervous system occurs during embryogenesis and requires a precise balance between stem cell proliferation, neuronal commitment to specific fates, and further differentiation. Understanding the cellular and molecular mechanisms regulating this balance in the embryonic brain is challenging. Here we reveal how the neurogenic capacity in the hindbrain is differently allocated to distinct domains over time, and how the boundary cells undergo a functional transition to become neurogenic during zebrafish hindbrain segmentation. By generating a CRISPR-based knock-in transgenic line to specifically label the boundary cell population, we tracked their derivatives over time and followed their behavior, allowing us to identify how asymmetric cell divisions arise and to reconstruct the trajectories of the boundary derivatives through the progenitor and differentiated domains. The behavioral switch in boundary cells is triggered by the onset of Notch signaling, based on lateral inhibition at the dorsoventral level. Our findings reveal that distinct neurogenic phases take place during hindbrain growth and suggest that boundary cells contribute to refine the final number, identity, and proportion of neurons in the brain.